Mercurial > repos > devteam > subtract_query
view subtract_query.py @ 2:659a1c095357 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
author | devteam |
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date | Fri, 18 Dec 2015 19:39:32 -0500 |
parents | df4bce472400 |
children | f58ba0382c26 |
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#!/usr/bin/env python # Greg Von Kuster """ Subtract an entire query from another query usage: %prog in_file_1 in_file_2 begin_col end_col output --ignore-empty-end-cols: ignore empty end columns when subtracting """ import sys from bx.cookbook import doc_optparse # Older py compatibility try: set() except: from sets import Set as set assert sys.version_info[:2] >= ( 2, 4 ) def get_lines(fname, begin_col='', end_col='', ignore_empty_end_cols=False): lines = set([]) i = 0 for i, line in enumerate(file(fname)): line = line.rstrip('\r\n') if line and not line.startswith('#'): if begin_col and end_col: """Both begin_col and end_col must be integers at this point.""" try: line = line.split('\t') line = '\t'.join([line[j] for j in range(begin_col - 1, end_col)]) if ignore_empty_end_cols: # removing empty fields, we do not compare empty fields at the end of a line. line = line.rstrip() lines.add( line ) except: pass else: if ignore_empty_end_cols: # removing empty fields, we do not compare empty fields at the end of a line. line = line.rstrip() lines.add( line ) if i: return (i + 1, lines) else: return (i, lines) def main(): # Parsing Command Line here options, args = doc_optparse.parse( __doc__ ) try: inp1_file, inp2_file, begin_col, end_col, out_file = args except: doc_optparse.exception() begin_col = begin_col.strip() end_col = end_col.strip() if begin_col != 'None' or end_col != 'None': """ The user selected columns for restriction. We'll allow default values for both begin_col and end_col as long as the user selected at least one of them for restriction. """ if begin_col == 'None': begin_col = end_col elif end_col == 'None': end_col = begin_col begin_col = int(begin_col) end_col = int(end_col) """Make sure that begin_col <= end_col (switch if not)""" if begin_col > end_col: tmp_col = end_col end_col = begin_col begin_col = tmp_col else: begin_col = end_col = '' try: fo = open(out_file, 'w') except: print >> sys.stderr, "Unable to open output file" sys.exit() """ len1 is the number of lines in inp1_file lines1 is the set of unique lines in inp1_file diff1 is the number of duplicate lines removed from inp1_file """ len1, lines1 = get_lines(inp1_file, begin_col, end_col, options.ignore_empty_end_cols) diff1 = len1 - len(lines1) len2, lines2 = get_lines(inp2_file, begin_col, end_col, options.ignore_empty_end_cols) lines1.difference_update(lines2) """lines1 is now the set of unique lines in inp1_file - the set of unique lines in inp2_file""" for line in lines1: print >> fo, line fo.close() info_msg = 'Subtracted %d lines. ' % ((len1 - diff1) - len(lines1)) if begin_col and end_col: info_msg += 'Restricted to columns c' + str(begin_col) + ' thru c' + str(end_col) + '. ' if diff1 > 0: info_msg += 'Eliminated %d duplicate/blank/comment/invalid lines from first query.' % diff1 print info_msg if __name__ == "__main__": main()